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AutoStitcher：一种用于从组织碎片中高效、稳健重建数字化全组织切片的自动化程序。

AutoStitcher: An Automated Program for Efficient and Robust Reconstruction of Digitized Whole Histological Sections from Tissue Fragments.

机构信息

Case Western Reserve University, Department of Biomedical Engineering, Cleveland OH, 44106, USA.

University of Pennsylvania, Department of Pathology, Philadelphia PA, 19104, USA.

出版信息

Sci Rep. 2016 Jul 26;6:29906. doi: 10.1038/srep29906.

DOI:10.1038/srep29906
PMID:27457670
原文链接:https://pmc.ncbi.nlm.nih.gov/articles/PMC4960603/
Abstract

In applications involving large tissue specimens that have been sectioned into smaller tissue fragments, manual reconstruction of a "pseudo whole-mount" histological section (PWMHS) can facilitate (a) pathological disease annotation, and (b) image registration and correlation with radiological images. We have previously presented a program called HistoStitcher, which allows for more efficient manual reconstruction than general purpose image editing tools (such as Photoshop). However HistoStitcher is still manual and hence can be laborious and subjective, especially when doing large cohort studies. In this work we present AutoStitcher, a novel automated algorithm for reconstructing PWMHSs from digitized tissue fragments. AutoStitcher reconstructs ("stitches") a PWMHS from a set of 4 fragments by optimizing a novel cost function that is domain-inspired to ensure (i) alignment of similar tissue regions, and (ii) contiguity of the prostate boundary. The algorithm achieves computational efficiency by performing reconstruction in a multi-resolution hierarchy. Automated PWMHS reconstruction results (via AutoStitcher) were quantitatively and qualitatively compared to manual reconstructions obtained via HistoStitcher for 113 prostate pathology sections. Distances between corresponding fiducials placed on each of the automated and manual reconstruction results were between 2.7%-3.2%, reflecting their excellent visual similarity.

摘要

在涉及已被分割成较小组织片段的大型组织标本的应用中，手动重建“伪全组织”组织学切片（PWMHS）可以促进（a）病理疾病注释，以及（b）图像配准和与放射图像的相关性。我们之前提出了一个名为 HistoStitcher 的程序，它允许比通用图像编辑工具（如 Photoshop）更有效地进行手动重建。然而，HistoStitcher 仍然是手动的，因此可能会很繁琐和主观，尤其是在进行大型队列研究时。在这项工作中，我们提出了 AutoStitcher，这是一种从数字化组织片段重建 PWMHS 的新型自动化算法。AutoStitcher 通过优化一种新的基于领域的成本函数来重建（“缝合”）一组 4 个片段的 PWMHS，以确保（i）相似组织区域的对齐，以及（ii）前列腺边界的连续性。该算法通过在多分辨率层次结构中执行重建来实现计算效率。对 113 个前列腺病理学切片进行了定量和定性比较，比较了通过 AutoStitcher 进行的自动 PWMHS 重建结果与通过 HistoStitcher 获得的手动重建结果。放置在每个自动和手动重建结果上的对应基准之间的距离在 2.7%-3.2%之间，反映了它们极好的视觉相似性。

https://cdn.ncbi.nlm.nih.gov/pmc/blobs/0228/4960603/549f6eb71df8/srep29906-f8.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/0228/4960603/07f10efc2e1d/srep29906-f1.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/0228/4960603/bfe497b64022/srep29906-f2.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/0228/4960603/d3b6baa8a546/srep29906-f3.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/0228/4960603/19792b9d3ded/srep29906-f4.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/0228/4960603/e9cd5fd63178/srep29906-f5.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/0228/4960603/1116f539fe8e/srep29906-f6.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/0228/4960603/a890c74020bb/srep29906-f7.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/0228/4960603/549f6eb71df8/srep29906-f8.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/0228/4960603/07f10efc2e1d/srep29906-f1.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/0228/4960603/bfe497b64022/srep29906-f2.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/0228/4960603/d3b6baa8a546/srep29906-f3.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/0228/4960603/19792b9d3ded/srep29906-f4.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/0228/4960603/e9cd5fd63178/srep29906-f5.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/0228/4960603/1116f539fe8e/srep29906-f6.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/0228/4960603/a890c74020bb/srep29906-f7.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/0228/4960603/549f6eb71df8/srep29906-f8.jpg

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本文引用的文献

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3D prostate histology image reconstruction: Quantifying the impact of tissue deformation and histology section location.3D前列腺组织学图像重建：量化组织变形和组织学切片位置的影响。
J Pathol Inform. 2013 Oct 31;4:31. doi: 10.4103/2153-3539.120874. eCollection 2013.
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HistoStitcher(©): an interactive program for accurate and rapid reconstruction of digitized whole histological sections from tissue fragments.
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PLoS One. 2018 Aug 31;13(8):e0200730. doi: 10.1371/journal.pone.0200730. eCollection 2018.
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